Spearheaded By Lourdes González-Vinceiro. We validated PLAMseq with CTCF & RNApol II and outperformed reference ChIPseq data from ENCODE. Used to characterize Histone H1 sumoylation and saw that it promotes interaction with SETDB1 and co-localization with H3K9me3 in specific repetitive regions.
April 28, 2025 at 7:55 AM
Spearheaded By Lourdes González-Vinceiro. We validated PLAMseq with CTCF & RNApol II and outperformed reference ChIPseq data from ENCODE. Used to characterize Histone H1 sumoylation and saw that it promotes interaction with SETDB1 and co-localization with H3K9me3 in specific repetitive regions.
Why then are there so many papers suggesting the opposite? It turns out that one widely used antibody (used also by the ENCODE consortium) also detects binding at CTCF sites. Other antibodies (and our ZNF143-HA tagged ChIPseq experiments) did not detect binding at CTCF sites.
December 20, 2024 at 4:22 PM
Why then are there so many papers suggesting the opposite? It turns out that one widely used antibody (used also by the ENCODE consortium) also detects binding at CTCF sites. Other antibodies (and our ZNF143-HA tagged ChIPseq experiments) did not detect binding at CTCF sites.
🌟 "I am the ReMap guy…" 🌟
ReMap is your go-to ChIP-seq database, mapping TFs, co-factors & chromatin regulators across genomes. High-res, open-access binding landscapes for human, mouse & more. Ready to explore gene regulation?
🧬 remap.univ-amu.fr
#Genomics #Bioinformatics #ChIPseq
ReMap is your go-to ChIP-seq database, mapping TFs, co-factors & chromatin regulators across genomes. High-res, open-access binding landscapes for human, mouse & more. Ready to explore gene regulation?
🧬 remap.univ-amu.fr
#Genomics #Bioinformatics #ChIPseq
November 22, 2024 at 2:02 PM
🌟 "I am the ReMap guy…" 🌟
ReMap is your go-to ChIP-seq database, mapping TFs, co-factors & chromatin regulators across genomes. High-res, open-access binding landscapes for human, mouse & more. Ready to explore gene regulation?
🧬 remap.univ-amu.fr
#Genomics #Bioinformatics #ChIPseq
ReMap is your go-to ChIP-seq database, mapping TFs, co-factors & chromatin regulators across genomes. High-res, open-access binding landscapes for human, mouse & more. Ready to explore gene regulation?
🧬 remap.univ-amu.fr
#Genomics #Bioinformatics #ChIPseq
🧪Move over CUT&Tag, there’s a new #TranscriptionFactor mapping method in town.
Our newly developed DynaTag is faster, cleaner, more sensitive than #ChIPseq, #CUT&RUN and #CUT&Tag.
🔗 Our @natcomms.nature.com paper: www.nature.com/articles/s41...
🧵Let’s break down what makes DynaTag so powerful (1/7)
Our newly developed DynaTag is faster, cleaner, more sensitive than #ChIPseq, #CUT&RUN and #CUT&Tag.
🔗 Our @natcomms.nature.com paper: www.nature.com/articles/s41...
🧵Let’s break down what makes DynaTag so powerful (1/7)
July 28, 2025 at 9:10 AM
🧪Move over CUT&Tag, there’s a new #TranscriptionFactor mapping method in town.
Our newly developed DynaTag is faster, cleaner, more sensitive than #ChIPseq, #CUT&RUN and #CUT&Tag.
🔗 Our @natcomms.nature.com paper: www.nature.com/articles/s41...
🧵Let’s break down what makes DynaTag so powerful (1/7)
Our newly developed DynaTag is faster, cleaner, more sensitive than #ChIPseq, #CUT&RUN and #CUT&Tag.
🔗 Our @natcomms.nature.com paper: www.nature.com/articles/s41...
🧵Let’s break down what makes DynaTag so powerful (1/7)
H3NGST: a fully automated, web-based platform for end-to-end ChIP-seq analysis. #ChIPseq #WebTool #Bioinformatics #Genomics #BMCbioinformatics 🧪🧬 🖥️
bmcbioinformatics.biomedcentral.com/articles/10....
bmcbioinformatics.biomedcentral.com/articles/10....
October 27, 2025 at 4:03 PM
H3NGST: a fully automated, web-based platform for end-to-end ChIP-seq analysis. #ChIPseq #WebTool #Bioinformatics #Genomics #BMCbioinformatics 🧪🧬 🖥️
bmcbioinformatics.biomedcentral.com/articles/10....
bmcbioinformatics.biomedcentral.com/articles/10....
🎉 The wait is over — say hello to the TIP-ChIP™ Assay Kit! [https://bit.ly/47Fpvjf] A high-throughput, low-input alternative to traditional ChIP that streamlines your workflow and boosts your data quality.
_____
#TIPChIP #Epigenetics #ChIPSeq #NGS #MolecularBiology #LabTools #Genomics #ActiveMotif
_____
#TIPChIP #Epigenetics #ChIPSeq #NGS #MolecularBiology #LabTools #Genomics #ActiveMotif
November 13, 2025 at 10:19 PM
🎉 The wait is over — say hello to the TIP-ChIP™ Assay Kit! [https://bit.ly/47Fpvjf] A high-throughput, low-input alternative to traditional ChIP that streamlines your workflow and boosts your data quality.
_____
#TIPChIP #Epigenetics #ChIPSeq #NGS #MolecularBiology #LabTools #Genomics #ActiveMotif
_____
#TIPChIP #Epigenetics #ChIPSeq #NGS #MolecularBiology #LabTools #Genomics #ActiveMotif
Overexpression of this PLDLS-inhibitor peptide in MUTZ3 cells results in (1) the loss of EVI1-CTBP1/2 interaction (by IP-WB) and (2) loss of detectable CTBP2 binding to chromatin (like EVI1 K.D. did), while the control (PLASS) did not have this effect.
On the right a chipseq plot of a target gene.
On the right a chipseq plot of a target gene.
May 16, 2024 at 1:29 PM
Overexpression of this PLDLS-inhibitor peptide in MUTZ3 cells results in (1) the loss of EVI1-CTBP1/2 interaction (by IP-WB) and (2) loss of detectable CTBP2 binding to chromatin (like EVI1 K.D. did), while the control (PLASS) did not have this effect.
On the right a chipseq plot of a target gene.
On the right a chipseq plot of a target gene.
Join us Oct. 28–30 for a Virtual ChIP-Seq / ATAC-Seq Workshop! 🧬
📅 10 AM – 2 PM EST
💻 Live on Zoom + recordings
💰 $500 ($400 UConn affiliates)
Register: bioinformatics.uconn.edu/cbc-workshops/
#ChIPSeq #ATACSeq #Bioinformatics #Workshop
📅 10 AM – 2 PM EST
💻 Live on Zoom + recordings
💰 $500 ($400 UConn affiliates)
Register: bioinformatics.uconn.edu/cbc-workshops/
#ChIPSeq #ATACSeq #Bioinformatics #Workshop
September 25, 2025 at 11:53 PM
Join us Oct. 28–30 for a Virtual ChIP-Seq / ATAC-Seq Workshop! 🧬
📅 10 AM – 2 PM EST
💻 Live on Zoom + recordings
💰 $500 ($400 UConn affiliates)
Register: bioinformatics.uconn.edu/cbc-workshops/
#ChIPSeq #ATACSeq #Bioinformatics #Workshop
📅 10 AM – 2 PM EST
💻 Live on Zoom + recordings
💰 $500 ($400 UConn affiliates)
Register: bioinformatics.uconn.edu/cbc-workshops/
#ChIPSeq #ATACSeq #Bioinformatics #Workshop
Unlock the power of ChIP-Seq — without the hassle. [https://bit.ly/4qMMDnp]
What is ChIP?
🧪 ChIP is a powerful method to study protein-DNA interactions and to investigate the locations of histone modifications across the genome.
___________
#ChIPSeq #Epigenetics #Genomics #ActiveMotif #ChIP30
What is ChIP?
🧪 ChIP is a powerful method to study protein-DNA interactions and to investigate the locations of histone modifications across the genome.
___________
#ChIPSeq #Epigenetics #Genomics #ActiveMotif #ChIP30
November 7, 2025 at 8:52 PM
Unlock the power of ChIP-Seq — without the hassle. [https://bit.ly/4qMMDnp]
What is ChIP?
🧪 ChIP is a powerful method to study protein-DNA interactions and to investigate the locations of histone modifications across the genome.
___________
#ChIPSeq #Epigenetics #Genomics #ActiveMotif #ChIP30
What is ChIP?
🧪 ChIP is a powerful method to study protein-DNA interactions and to investigate the locations of histone modifications across the genome.
___________
#ChIPSeq #Epigenetics #Genomics #ActiveMotif #ChIP30
Looking for #Epigenetics Data Analysis? We offer a range of services including #ChIPseq analysis & #DNAMethylation. Learn more at: www.fiosgenomics.com/service/epig...
July 18, 2025 at 10:35 AM
Looking for #Epigenetics Data Analysis? We offer a range of services including #ChIPseq analysis & #DNAMethylation. Learn more at: www.fiosgenomics.com/service/epig...
🧪Move over CUT&Tag, there’s a new #TranscriptionFactor mapping method in town.
The newly developed DynaTag by Robert and his lab @epistrucstab.bsky.social is faster, cleaner, more sensitive than #ChIPseq, #CUT&RUN and #CUT&Tag.
🔗 Our @natcomms.nature.com paper: www.nature.com/articles/s41...
The newly developed DynaTag by Robert and his lab @epistrucstab.bsky.social is faster, cleaner, more sensitive than #ChIPseq, #CUT&RUN and #CUT&Tag.
🔗 Our @natcomms.nature.com paper: www.nature.com/articles/s41...
July 28, 2025 at 9:04 AM
🧪Move over CUT&Tag, there’s a new #TranscriptionFactor mapping method in town.
The newly developed DynaTag by Robert and his lab @epistrucstab.bsky.social is faster, cleaner, more sensitive than #ChIPseq, #CUT&RUN and #CUT&Tag.
🔗 Our @natcomms.nature.com paper: www.nature.com/articles/s41...
The newly developed DynaTag by Robert and his lab @epistrucstab.bsky.social is faster, cleaner, more sensitive than #ChIPseq, #CUT&RUN and #CUT&Tag.
🔗 Our @natcomms.nature.com paper: www.nature.com/articles/s41...
New preprint from the @arnausebe.bsky.social lab! 💐
Here @crisnava.bsky.social, @seanamontgomery.bsky.social & collaborators develop a novel ChIPseq protocol, and demonstrate its huge potential to study the evolution of chromatin function and regulation across the eukaryotic tree of life.
Here @crisnava.bsky.social, @seanamontgomery.bsky.social & collaborators develop a novel ChIPseq protocol, and demonstrate its huge potential to study the evolution of chromatin function and regulation across the eukaryotic tree of life.
March 19, 2025 at 10:31 AM
New preprint from the @arnausebe.bsky.social lab! 💐
Here @crisnava.bsky.social, @seanamontgomery.bsky.social & collaborators develop a novel ChIPseq protocol, and demonstrate its huge potential to study the evolution of chromatin function and regulation across the eukaryotic tree of life.
Here @crisnava.bsky.social, @seanamontgomery.bsky.social & collaborators develop a novel ChIPseq protocol, and demonstrate its huge potential to study the evolution of chromatin function and regulation across the eukaryotic tree of life.
Looking for #Epigenetics Data Analysis? We offer a range of services including #ChIPseq analysis & #DNAMethylation. Learn more at www.fiosgenomics.com/services/epi...
March 25, 2025 at 11:55 AM
Looking for #Epigenetics Data Analysis? We offer a range of services including #ChIPseq analysis & #DNAMethylation. Learn more at www.fiosgenomics.com/services/epi...
Yeah you are absolutely right. I'll rephrase it as it wasn't clear, my bad. What i meant is all baseline models bassnet/enformer/borzoi and so on are trained on different cell types with epigenetic data on bulk measures (ChIPseq, DNAse, ...). I was wondering whether re-training them w/ data
November 29, 2024 at 9:26 AM
Yeah you are absolutely right. I'll rephrase it as it wasn't clear, my bad. What i meant is all baseline models bassnet/enformer/borzoi and so on are trained on different cell types with epigenetic data on bulk measures (ChIPseq, DNAse, ...). I was wondering whether re-training them w/ data
TBX4 in human Lung Pericyte & Fibroblast (matrix, motility, guidance molecules, cell cycle)
scRNAseq developing mouse lung
Bulk RNAseq + ChIPseq cultured human lung pericyte & fibroblast -/+ siTBX4
#PulmCirc 2025
onlinelibrary.wiley.com/doi/10.1002/...
scRNAseq developing mouse lung
Bulk RNAseq + ChIPseq cultured human lung pericyte & fibroblast -/+ siTBX4
#PulmCirc 2025
onlinelibrary.wiley.com/doi/10.1002/...
March 4, 2025 at 7:48 PM
TBX4 in human Lung Pericyte & Fibroblast (matrix, motility, guidance molecules, cell cycle)
scRNAseq developing mouse lung
Bulk RNAseq + ChIPseq cultured human lung pericyte & fibroblast -/+ siTBX4
#PulmCirc 2025
onlinelibrary.wiley.com/doi/10.1002/...
scRNAseq developing mouse lung
Bulk RNAseq + ChIPseq cultured human lung pericyte & fibroblast -/+ siTBX4
#PulmCirc 2025
onlinelibrary.wiley.com/doi/10.1002/...
IMO foundational models need to take in-vivo atlases as the main data to explain, while using
biophysical data (eg HT-SELEX, ELISA-style, Y2H PPI),
in-vitro model data,
cancer cell line data (eg ChIPseq)
to inform a specific subset of parameters that can be justifiably derived from those data.
biophysical data (eg HT-SELEX, ELISA-style, Y2H PPI),
in-vitro model data,
cancer cell line data (eg ChIPseq)
to inform a specific subset of parameters that can be justifiably derived from those data.
January 28, 2025 at 11:50 PM
IMO foundational models need to take in-vivo atlases as the main data to explain, while using
biophysical data (eg HT-SELEX, ELISA-style, Y2H PPI),
in-vitro model data,
cancer cell line data (eg ChIPseq)
to inform a specific subset of parameters that can be justifiably derived from those data.
biophysical data (eg HT-SELEX, ELISA-style, Y2H PPI),
in-vitro model data,
cancer cell line data (eg ChIPseq)
to inform a specific subset of parameters that can be justifiably derived from those data.
For this manuscript, all lab data & alphafold predictions are deposited on ZENODO for #OpenScience: https://zenodo.org/records/10650341; and proteomics data under PXD043333 & PXD048760 (proteomeXchange) and chipseq tracks on GEO (GSE236010)
May 16, 2024 at 1:29 PM
For this manuscript, all lab data & alphafold predictions are deposited on ZENODO for #OpenScience: https://zenodo.org/records/10650341; and proteomics data under PXD043333 & PXD048760 (proteomeXchange) and chipseq tracks on GEO (GSE236010)
Plant pathogens! @karchuntan.bsky.social on regulation of the effector arsenal in Septoria. ChipSeq and RNA seq show that Pf2 TF is a regulator of >400 proteins (of which >60 are positively regulated), including many transporters and other TFs!
#ecfg17
#ecfg17
March 4, 2025 at 2:12 PM
Plant pathogens! @karchuntan.bsky.social on regulation of the effector arsenal in Septoria. ChipSeq and RNA seq show that Pf2 TF is a regulator of >400 proteins (of which >60 are positively regulated), including many transporters and other TFs!
#ecfg17
#ecfg17
New preprint from the Lab at @cabimer.bsky.social. We present PLAMseq, using TurboID to do like ChIPseq and proximity proteomics in the same protocol with extra powers like mapping protein interactions in the genome.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
PLAMseq enables the proteo-genomic characterization of chromatin-associated proteins and protein interactions in a single experimental workflow.
Chromatin Immunoprecipitation (ChIP) and Co-Immunoprecipitation (CoIP) assays are the most common approaches to characterize the genomic localization and protein interactors, respectively, for a prote...
www.biorxiv.org
April 28, 2025 at 7:55 AM
New preprint from the Lab at @cabimer.bsky.social. We present PLAMseq, using TurboID to do like ChIPseq and proximity proteomics in the same protocol with extra powers like mapping protein interactions in the genome.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Here's an update on our story of doing CHIPSeq for the Huntingtin protein. Really interesting stuff, as it suggests HTT is binding to chromatin in patterns that are coherent with gene expression changes in HD, suggesting HTT might play a direct role in these changes.
Promoting this freshly revised HTT-chromatin interaction preprint that I've been working on with @jcarroll42.bsky.social as my first skeet. www.biorxiv.org/content/10.1...
January 7, 2025 at 7:49 PM
Here's an update on our story of doing CHIPSeq for the Huntingtin protein. Really interesting stuff, as it suggests HTT is binding to chromatin in patterns that are coherent with gene expression changes in HD, suggesting HTT might play a direct role in these changes.
chatomics! Calculating Counts per Million (CPM) for RNAseq or ChIPseq data www.youtube.com/watchv=LxToa... #bioinformatics
December 3, 2024 at 2:15 PM
chatomics! Calculating Counts per Million (CPM) for RNAseq or ChIPseq data www.youtube.com/watchv=LxToa... #bioinformatics
ChIPseq says yes, but we needed another test.
The model told us an IkBe knockout would selectively upregulate cRel, which would upregulate MCL1 if we were right.
Collaborating with Alexander Hoffmann's group we tested this in IkBe KO mice.
cRel and MCL1 go up!
The model told us an IkBe knockout would selectively upregulate cRel, which would upregulate MCL1 if we were right.
Collaborating with Alexander Hoffmann's group we tested this in IkBe KO mice.
cRel and MCL1 go up!
December 6, 2024 at 6:18 PM
ChIPseq says yes, but we needed another test.
The model told us an IkBe knockout would selectively upregulate cRel, which would upregulate MCL1 if we were right.
Collaborating with Alexander Hoffmann's group we tested this in IkBe KO mice.
cRel and MCL1 go up!
The model told us an IkBe knockout would selectively upregulate cRel, which would upregulate MCL1 if we were right.
Collaborating with Alexander Hoffmann's group we tested this in IkBe KO mice.
cRel and MCL1 go up!
But otherwise - for the vast majority of things in our collection, if you sequence it or do RNAseq, chipseq or whatever, that data is your data. Have fun! The Data Use Agreement from ATCC only applies to data we produce from our materials. It allows noncommercial research use of our data.
November 21, 2024 at 3:09 PM
But otherwise - for the vast majority of things in our collection, if you sequence it or do RNAseq, chipseq or whatever, that data is your data. Have fun! The Data Use Agreement from ATCC only applies to data we produce from our materials. It allows noncommercial research use of our data.
my main prob with Ancestry (and 23andMe) is they reserve the right to do 100X whole-genome sequencing on you if you pop something "interesting" on their chipseq test, and then once they do that they don't have to tell you SHIT about what they learn, and never will
June 6, 2024 at 4:43 AM
my main prob with Ancestry (and 23andMe) is they reserve the right to do 100X whole-genome sequencing on you if you pop something "interesting" on their chipseq test, and then once they do that they don't have to tell you SHIT about what they learn, and never will
When speaking to scientists this is definitely not the comparison I would go for.
"CHIPseq, the Bitcoin of biology" lol.
"CHIPseq, the Bitcoin of biology" lol.
December 21, 2024 at 12:02 AM
When speaking to scientists this is definitely not the comparison I would go for.
"CHIPseq, the Bitcoin of biology" lol.
"CHIPseq, the Bitcoin of biology" lol.